How can I know abundances of different genes in metagenome samples?
I found "Abundance profiles" paragraph in MG RAST server manual (ftp://ftp.metagenomics.anl.gov/data/manual/mg-rast-manual.pdf page 13), but there is only written about how MG RAST computes it, not about how to get this data... I just want to get numbers of copies of each annotated gene, founded in given metagenome sample.
You can expand 'Metagenomes section', pick the one you are interested in and then click 'load data' below. You can load one more, as Data B (change at the top).
On the right, just above the graphics, there is a button 'export kegg abundance'. After you click it, new window will show - with the abundances you searched for. It is possible to save them from there ('Click to save as tab-delimited text file' at the top).
You can go to "Metagenome Analysis" page and select the metagenome you're interested in. Then you can choose the annotation method and database, let's say, "Functional Abundance" →"Hierarchical Classification"→"Annotation source"=KO
Now you can generate the table and get the annotation/gene abundance, and download this table if necessary.